On Thursday, July 25, 2013 3:55:08 PM UTC+1, Christoph Junghans wrote: > > 2013/7/25 <[email protected] <javascript:>>: > > And how g_rdf tool of gromacs will know which groups to use from > index.ndx ? > That was one of the reason to deprecate g_rdf and make csg_stat the > default. VOTCA uses types not energy groups. > > Back in 2011, we used the following script: > < > https://code.google.com/p/votca/source/browse/share/scripts/inverse/calc_rdf_gromacs.sh?repo=csg&name=a3e6095e3ee6> > > > This could serve as basis for your myrdf.sh >
Thanks a lot! So If use the script above with gromacs.g_rdf.opts -fade VALUE in my xml file I would be able to get what I want? Sorry, dont have have scripting experience :( Steven > > > > Steven > > > > > > On Monday, July 15, 2013 12:02:00 PM UTC+1, [email protected] wrote: > >> > >> Dear Votca Users, > >> > >> I have to issues with IBI: > >> > >> 1) I took one my ditributions and calculated on my own potential W= > -kBT > >> ln(RDF) and I got different potential than Votca provide me. For > instance > >> lets calculate the potential minimum for the distribution maximum of > 162. > >> Pot = -.249435*ln(164) = -12.69. The minimum of Votca potential > corresponds > >> to approximately -16 kJ/mol. Where I missed something? is it somehow > >> normalized? > >> > >> 2) After 1st iteration my distribution was much higher than the target > one > >> so I guess the potential should decrease but apparently the new > potential > >> has deeper minima so the next distribution has a even higer > distribution. > >> Could anyone please explain me this? > >> > >> Steven > >> > >> > > -- > > You received this message because you are subscribed to the Google > Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to [email protected] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
